Seqanswers Leaderboard Ad

Collapse

Announcement

Collapse
No announcement yet.
X
 
  • Filter
  • Time
  • Show
Clear All
new posts

  • Gene Prediction: AUGUSTUS

    Hello All,

    I have sequenced and assembled the chloroplast genome of a red alga. I would like to use AUGUSTUS for gene prediction within my genome; however, I would like to choose an organism model as close to my species as possible. Does anyone know if there's a way to specify an organism model that's not already listed in AUGUSTUS? The model organisms I would like to use have fully assembled and annotated genomes.

    Thanks!

    - Amanda G

  • #2
    If it is not yet available in AUGUSTUS, you may submit a new training request online: http://bioinf.uni-greifswald.de/weba...raining/create

    Comment


    • #3
      I'm trying to train and predict UTR in transcriptome using Augustus.
      I'm following the script autoAug.pl (in augustus.2.5.5 version).


      My command line:
      sudo AUGUSTUS_CONFIG_PATH=home/augustus.2.5.5/config perl
      /home/augustus.2.5.5/scripts/autoAug.pl --species=myspecie
      --genome=genome.fa --trainingset=merged_annotations.gff --cdna=transc.fasta
      -v --noninteractive --workingdir=/home/jordana/teste25 > GFF_step1

      But, in first step (-- Construct an initial training set of genes (protein
      coding regions thereof), e.g. using PASA) there are a something that stoped
      the script. And every attempt the log (GFF_step1 file) returns and stop in
      this part "2 First try with etraining: etraining --species=myspecie
      training.gb.train >train.out ...". Furthermore, below command line appear
      just "failed to execute:".

      I also tried use another data set (e.g. human genome and genbank human
      genome), but I had the same problem. And I not have ideia what happens.

      Comment


      • #4
        Hello,

        I want to predict gene in buffalo dataset, which training dataset should I use? Do I need to train cattle data or human training dataset will work?

        Thanks
        Anand Patel

        Comment

        Latest Articles

        Collapse

        • seqadmin
          Strategies for Sequencing Challenging Samples
          by seqadmin


          Despite advancements in sequencing platforms and related sample preparation technologies, certain sample types continue to present significant challenges that can compromise sequencing results. Pedro Echave, Senior Manager of the Global Business Segment at Revvity, explained that the success of a sequencing experiment ultimately depends on the amount and integrity of the nucleic acid template (RNA or DNA) obtained from a sample. “The better the quality of the nucleic acid isolated...
          03-22-2024, 06:39 AM
        • seqadmin
          Techniques and Challenges in Conservation Genomics
          by seqadmin



          The field of conservation genomics centers on applying genomics technologies in support of conservation efforts and the preservation of biodiversity. This article features interviews with two researchers who showcase their innovative work and highlight the current state and future of conservation genomics.

          Avian Conservation
          Matthew DeSaix, a recent doctoral graduate from Kristen Ruegg’s lab at The University of Colorado, shared that most of his research...
          03-08-2024, 10:41 AM

        ad_right_rmr

        Collapse

        News

        Collapse

        Topics Statistics Last Post
        Started by seqadmin, Yesterday, 06:37 PM
        0 responses
        10 views
        0 likes
        Last Post seqadmin  
        Started by seqadmin, Yesterday, 06:07 PM
        0 responses
        9 views
        0 likes
        Last Post seqadmin  
        Started by seqadmin, 03-22-2024, 10:03 AM
        0 responses
        51 views
        0 likes
        Last Post seqadmin  
        Started by seqadmin, 03-21-2024, 07:32 AM
        0 responses
        67 views
        0 likes
        Last Post seqadmin  
        Working...
        X